I guess i am a liitle confused then. This will all be in watch form. So i cant unplug the batteries all the time. So what will happen when it is being run by batteries then I plug it in to charge it? Will it get twice the voltage? I thought it had to have that circuite in there just like a cell phone when you plug and unplug it. Sorry i just dont understand.

I plan on majing this watch solid brass and once it is pit together batteries wont be very easily excessible.That would work but i plan on this being like a cellphone. I dont want to have to swap batteries.

the only battery I see in that post is a 400 mAh Li-ion battery sitting next to the PCB.If the battery is fixed, there's no real need for a supercap either. It doesn't add much time for your timekeeping if you run out of battery (and the RTC can do with as little as 1.3V or so, when your processor stopped working already - maybe even the boost converter). Can connect the battery backup pin directly to the main battery.

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I found this battery at Adafruit. Comfortable fit under the display. A bit bigger capacity has this battery which would fit next to the display, broad side, making for an overall PCB size of 20x40 mm, and an overall thickness of about 15 mm.

The battery will cut off at 3V so a supercap would still come in useful to keep the time as the battery recharges.

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For the overall arrangement: the surface area needed for the components excluding supercap, battery, connectors and push buttons is a little more than the surface area of the display itself. Without battery, I had the supercap, buttons and display on one side of the PCB, the rest on the back - partly in between the pins of the display.The various through-hole components (the display itself, the supercap) do severely limit how things can be arranged, though.

Quality of answers is related to the quality of questions. Good questions will get good answers. Useless answers are a sign of a poor question.